The water quality of the river Ouse is compromised by a range of pressures, from isolated sources of pollution through to the combined effects of multiple diffuse sources, both rural and urban. Evidence driving the ecological status of the river system shows that nutrification, particularly phosphates in freshwaters, are a primary reasons for poor water quality.

Other factors affecting surface water quality include increased demand for drinking water, a growing population, the need to increase food production and the uncertainty of climate change factors.

Work has been ongoing for many years to help manage these pressures. In particular, significant investment by water companies has resulted in much reduced nutrient levels being discharging from large sewage treatment works. Additionally, best practice land management techniques have developed and are being used, often funded by agri-environment schemes.

The river has also been significantly modified over the centuries, resulting in canalisation, culverts, banking and other hard engineering, that have served the purpose of draining land for agriculture by speeding up the flow of water from the land to the sea. River flow and fluvial flooding can also be affected by the installation or removal of in-channel structures. These interventions have had an impact on the course and flow of the river and are contributing to a reduction in the ecological status of the system.